MANIFEST.in
setup.py
bin/aa-info.py
bin/aa-to-properties.py
bin/adaptor-distances.py
bin/alignments-per-read.py
bin/bit-score-to-e-value.py
bin/cat-json-blast-records.py
bin/check-fasta-json-blast-consistency.py
bin/codon-distance.py
bin/convert-blast-xml-to-json.py
bin/convert-diamond-to-json.py
bin/convert-fasta-to-one-sequence-per-line.py
bin/convert-fastq-to-fasta.py
bin/convert-sam-to-fastq.sh
bin/dna-to-aa.py
bin/e-value-to-bit-score.py
bin/extract-ORFs.py
bin/fasta-subset.py
bin/fasta-subtraction.py
bin/filter-fasta-by-complexity.py
bin/filter-fasta-by-taxonomy.py
bin/filter-fasta.py
bin/filter-hits-to-fasta.py
bin/find-hits.py
bin/get-features.py
bin/get-reads.py
bin/graph-evalues.py
bin/group-summary-proteins.py
bin/group-summary-viruses-html.py
bin/group-summary-viruses.py
bin/local-align.py
bin/noninteractive-alignment-panel.py
bin/position-summary.py
bin/pre-commit.sh
bin/print-blast-xml-for-derek.py
bin/print-blast-xml.py
bin/print-read-lengths.py
bin/randomize-fasta.py
bin/read-blast-json.py
bin/read-blast-xml.py
bin/sff-to-fastq.py
bin/split-fasta-by-adaptors.py
bin/summarize-reads.py
bin/trim-primers.py
bin/trim-reads.py
bin/write-htcondor-job-spec.py
dark/__init__.py
dark/aa.py
dark/alignments.py
dark/analyze_reads.py
dark/baseimage.py
dark/btop.py
dark/codonDistance.py
dark/consensus.py
dark/database.py
dark/dimension.py
dark/distance.py
dark/entrez.py
dark/fasta.py
dark/fasta_ss.py
dark/fastq.py
dark/features.py
dark/filter.py
dark/gor4.py
dark/graphics.py
dark/hsp.py
dark/html.py
dark/intervals.py
dark/ipynb.py
dark/local_align.py
dark/mutations.py
dark/ncbidb.py
dark/orfs.py
dark/reads.py
dark/score.py
dark/sequence.py
dark/simplify.py
dark/summarize.py
dark/taxonomy.py
dark/titles.py
dark/utils.py
dark/blast/__init__.py
dark/blast/alignments.py
dark/blast/conversion.py
dark/blast/hacks.py
dark/blast/hsp.py
dark/blast/params.py
dark/blast/records.py
dark/blast/score.py
dark/data/gor4/New_KS.267.obs
dark/data/gor4/New_KS.267.seq
dark/data/gor4/README.md
dark/data/gor4/new-gor4.obs
dark/data/gor4/new-gor4.seq
dark/diamond/__init__.py
dark/diamond/alignments.py
dark/diamond/conversion.py
dark/diamond/hsp.py
dark_matter.egg-info/PKG-INFO
dark_matter.egg-info/SOURCES.txt
dark_matter.egg-info/dependency_links.txt
dark_matter.egg-info/pbr.json
dark_matter.egg-info/requires.txt
dark_matter.egg-info/top_level.txt
src/gor4/api.c
src/gor4/build.py
src/gor4/defines.h
src/gor4/gor4-base.c
src/gor4/gor4-base.h
src/gor4/nrutil.c
src/gor4/nrutil.h
test/test_aa.py
test/test_alignments.py
test/test_analyze_reads.py
test/test_btop.py
test/test_codonDistance.py
test/test_dimension.py
test/test_distance.py
test/test_fasta.py
test/test_fasta_ss.py
test/test_fastq.py
test/test_features.py
test/test_filter.py
test/test_gor4.py
test/test_graphics.py
test/test_hsp.py
test/test_html.py
test/test_intervals.py
test/test_local_align.py
test/test_mutations.py
test/test_orfs.py
test/test_reads.py
test/test_score.py
test/test_sequence.py
test/test_simplify.py
test/test_summarize.py
test/test_taxonomy.py
test/test_titles.py
test/test_utils.py